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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 2qbc:B3001, See in JSmolMgRNA representative site for type 6BO            Click on the image to toggle views


Site type: 6Bout

Schematic drawing for
6Bout

MgRNA type 6BO
List of all 78 Mg2+ binding sites with the site type 6Bout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 1 of 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1jj2 08038 6Bout 03152, 03176, 03198, 03200, 07362, 08802 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1k73 A8038 6Bout A3620, A3644, A3666, A3668, A7826, A9281 G:A2271, G:A2275, U:A2115, U:A2116, A:A2274, U:A2276
1k8a A8038 6Bout A3216, A3239, A3261, A3263, A7363, A8876 U:A2116, G:A2271, G:A2275, U:A2276, A:A2274, U:A2115
1k9m A8038 6Bout A3617, A3640, A3662, A3664, A7824, A9281 U:A2116, G:A2271, G:A2275, A:A2274, U:A2115, U:A2276
1kqs 08038 6Bout 03134, 03157, 03179, 03181, 07297, 08796 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1m90 A8038 6Bout A3154, A3178, A3199, A3201, A7345, A8802 G:A2271, G:A2275, U:A2116, A:A2274, U:A2115, U:A2276
1n8r A8038 6Bout A4021, A4045, A4066, A4068, A8299, A9678 G:A2271, G:A2275, U:A2115, U:A2116, A:A2274, U:A2276
1q81 A8038 6Bout A3138, A3162, A3184, A3186, A7295, A8799 G:A2271, G:A2275, U:A2115, U:A2116, A:A2274, U:A2276
1q86 A8038 6Bout A3151, A3175, A3197, A3199, A7317, A8806 G:A2271, G:A2275, U:A2116, A:A2274, U:A2115, U:A2276
1qvf 08038 6Bout 03144, 03166, 03185, 03187, 07263, 08803 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1qvg 08038 6Bout 03130, 03155, 03176, 03178, 07195, 08807 G:02271, G:02275, U:02115, U:02116, A:02274, U:02276
1s72 08038 6Bout 03147, 03171, 03193, 03195, 07317, 08802 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vq4 08038 6Bout 03930, 03955, 03976, 03978, 07981, 09600 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vq5 08038 6Bout 03941, 03966, 03987, 03989, 08132, 09605 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vq6 08038 6Bout 03933, 03958, 03979, 03981, 07989, 09606 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vq7 08038 6Bout 03949, 03974, 03995, 03997, 08128, 09608 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vql 08038 6Bout 04218, 04241, 04262, 04264, 08341, 09906 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vqm 08038 6Bout 04226, 04248, 04269, 04271, 08341, 09908 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vqn 08038 6Bout 04221, 04245, 04267, 04269, 08333, 09906 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vqp 08038 6Bout 04237, 04261, 04282, 04284, 08361, 09909 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1vs8 B2905 6Bout B3014, B3015, B3016, B3017, B3018, B3019 G:B2238, G:B2242, U:B2243, A:B2241, U:B2074, U:B2075
1yhq 08028 6Bout 04121, 04146, 04168, 04170, 08325, 09780 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1yi2 08038 6Bout 03623, 03647, 03668, 03670, 07773, 09283 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1yij 08038 6Bout 03635, 03659, 03680, 03682, 07785, 09283 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
1yjn 08038 6Bout 03637, 03662, 03684, 03686, 07798, 09283 G:02271, G:02275, U:02115, U:02116, A:02274, U:02276

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"
Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen
cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform
Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].


Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>